calmate: Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

The CalMaTe method calibrates preprocessed allele-specific copy number estimates (ASCNs) from DNA microarrays by controlling for single-nucleotide polymorphism-specific allelic crosstalk. The resulting ASCNs are on average more accurate, which increases the power of segmentation methods for detecting changes between copy number states in tumor studies including copy neutral loss of heterozygosity. CalMaTe applies to any ASCNs regardless of preprocessing method and microarray technology, e.g. Affymetrix and Illumina.

Citing calmate

Whenever using the calmate package or the CalMaTe method, please cite:

• M. Ortiz-Estevez, A. Aramburu, H. Bengtsson, P. Neuvial, and A. Rubio, CalMaTe: A method and software to improve allele-specific copy number of SNP arrays for downstream segmentation, Bioinformatics, Volume 28, Issue 13, 2012, Pages 1793-1794, doi:10.1093/bioinformatics/bts248

Installation

R package calmate is available on CRAN and can be installed in R as:

install.packages("calmate")

Pre-release version

To install the pre-release version that is available in Git branch develop on GitHub, use:

remotes::install_github("HenrikBengtsson/calmate", ref="develop")

This will install the package from source.